CortexJDK handles the heavy lifting when operating with these data structures, permitting developers to concentrate on the genome analysis and variant calling tools that can be written on top of this API.

Additionally CortexJDK also contains the graph-based de novo mutation calling software developed during my D.Phil. These tools may be split into their own repository at a later date. For now, they serve as a useful example for other developers on how to use the API.